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Yorodumi- PDB-3huj: Crystal structure of human CD1d-alpha-Galactosylceramide in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3huj | |||||||||
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Title | Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / CD1d / NKT T cell receptor / alpha-galactosylceramide / protein receptor complex / Cell membrane / Disulfide bond / Endosome / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Innate immunity / Lysosome / Membrane / Transmembrane / Disease mutation / Glycation / MHC I / Pyrrolidone carboxylic acid / Secreted | |||||||||
Function / homology | Function and homology information lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / positive regulation of T cell proliferation / detection of bacterium / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / histone binding / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / intracellular iron ion homeostasis / amyloid fibril formation / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Pang, S.S. | |||||||||
Citation | Journal: Immunity / Year: 2009 Title: Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / ...Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / Matsuda, J.L. / Gapin, L. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3huj.cif.gz | 347.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3huj.ent.gz | 276.7 KB | Display | PDB format |
PDBx/mmJSON format | 3huj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3huj ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3huj | HTTPS FTP |
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-Related structure data
Related structure data | 3he6C 3he7C 2po6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 32324.383 Da / Num. of mol.: 2 / Fragment: UNP residues 21-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Cell line (production host): High-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769 |
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-NKT15 T cell receptor ... , 2 types, 4 molecules EGFH
#3: Protein | Mass: 23227.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #4: Protein | Mass: 28033.189 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Sugars , 4 types, 6 molecules
#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#6: Polysaccharide | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#7: Sugar | #8: Sugar | |
-Non-polymers , 2 types, 483 molecules
#9: Chemical | ChemComp-MG / |
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#10: Water | ChemComp-HOH / |
-Details
Sequence details | NO SUITABLE DATABASE REFERENCES WERE FOUND FOR CHAINS E, F, G AND H.(KJER-NIELSEN, L., BORG, N.A., ...NO SUITABLE DATABASE REFERENCES |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 66054 / Num. obs: 66054 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5344 / % possible all: 74.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2po6 Resolution: 2.5→47.28 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / SU B: 21.082 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.762 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→47.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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